M&I Week 2 Flashcards
Two Distinct Functions of Antibodies
Conferred by two distinct portions of the antibody. Variable region interacts with antigen. Constant region interacts with other components of the immune system, which mediate different effector functions of antibodies
Variable Region of the Antibody
Highly diverse among different antibodies and interacts with the antigen. Each antibody contains two that can bind with antigen
Number of Variable Regions in an Antibody
2
Constant Region of an Antibody and Isotypes
Each antibody has only one constant region and it interacts with other components of the immune system, which mediate distinct effector functions of antibodies. Comes in five different forms (IgM, IgG, IgA, and IgE), each specialized to activate distinct components of the immune system and thus elicit distinct effector functions
Number of Constant Regions in an Antibody
1 & 5 isotypes
B-Cell Differentiation
Naive B Cells start off with producing surface immunoglobulins of the IgM and IgD varieties (co-expressed). Upon antigen recognition and B Cell activation, these B cells might differentiate into plasma cells that secrete antibodies of the IgM variety. Can occur in a T Cell independent manner, but most require T Cell help
Somatic Hypermutation
Some activated B Cells that receive T Cell help will undergo somatic hypermutation that results in the introduction of point mutations within the variable region of the antibody, which ultimately results in the development of antibodies with increased affinity for antigen
Affinity Maturation of the Antibody Response
Somatic Hypermutation can lead to the development of antibodies with increased affinity for antigen, resulting in “affinity maturation of the antibody response”. Requires intimate interactions of B Cells with T Cells and of B Cells with antigens trapped by follicular dendritic cells in germinal centers of lymphoid organs
Germinal Center Reaction
Affinity maturation requires intimate interactions of B Cells with T Cells and B Cells with antigens trapped by follicular dendritic cells in germinal centers of lymphoid organs, a process referred to as the germinal center reaction
Class Switch Recombination
When B Cells switch their antibody class from IgM (and IgD) to one of the other classes, without altering their antigen-binding specificity, in a genetic process referred to as class switch recombination
Differentiation into Plasma Cells vs. Differentiation into Memory B Cells
Plasma cell differentiation is a terminal process, whereas memory B Cells can be reactivated by specific antigen and undergo further somatic hypermutation and class switch recombination
Shape of Antibodies
Y-shaped, the structure of the cell surface expressed form of an immunoglobulin is identical to that of the secreted form, except for a short hydrophobic portion in the carboxy terminus of the heavy chain that anchors the protein to the membrane
Number of Name of Polypeptide Chains (Antibodies)
Antibodies contain two types of polypeptide chains, termed a heavy (H) and light (L) chain. Each antibody contains two heavy chains and two light chains
How Are Heavy Chains Linked to Each Other
Disulfide bonds
How Are Heavy Chains Linked to Light Chains
Disulfide bonds
Two Types of Light Chains
Kappa and Lambda
Isotypic Exclusion
A given antibody contains either kappa or gamma light chains, but never one of each
What Determines the Class of an Antibody
The heavy chain of the antibody
Five Different Heavy Chains
Mu, delta, gamma, alpha, and episilon, which corresponds to the five classes of antibodies (IgM, IgD, IgA, IgE). Can also contain subtypes for each heavy chain
Two Isotypes of Antibody That Can Polymerize
IgM assembles as a pentamer and IgA can assemble as a dimer
J-Chain in Antibody Polymerization
Multimerization of IgM and IgA monomers is facilitated by interaction of a polypeptide called a J-Chain, with cysteine residues in the “tailpiece” of IgM and IgA
Functions of Multimer Antibodies (IgM and IgA)
IgM is the first antibody class to be synthesized and its pentameric form permits high avidity interactions with antigen; IgA plays an important role in mucosal immunity and its transport across mucosal membranes requires dimerization (usually present as a monomer in the blood and lymph)
H and L Chains Contain Multiple Domains of What Length and What Structure
110 amino acids in length which fold into a structure referred to as a Beta-Barrel (two anti-parallel Beta-sheets connected by a disulfide bond)
Immunoglobulin Fold
The particular beta-barrel structure adopted by an immunoglobulin domain. This type of fold is quite popular among proteins of the immune system (as well as the nervous system)
Which Termini of Heavy and Light Chains Are Highly Variable
The amino-termini of both the heavy and light chains of immunoglobulins are highly variable
Variable Domains of Heavy and Light Chains
Variability predominantly contained within the N-terminus immunoglobulin domains of the heavy and light chains, which are referred to as the variable domains of the heavy and light chains, Vh and Vl, and together form the variable region of an antibody
Constant Domains of the Heavy and Light Chains
The constant domains of the heavy and light chains (Ch and Cl) together form the constant domain of the antibody molecule. Individual domains within the constant region of the heavy chain are referred to as Ch1, Ch2, and so on
Papain
Protease that cleaves antibodies just above the disulfide bonds that connect the two heavy chains together, resulting in three fragments: two fragments called Fab fragments (Fragment antigen binding), are identical and can each interact with antigen, and the third fragment, called the Fc fragment (Fragment cystallizable) mediates the effector functions of an antibody. Differences between distinct antibody classes are largely contained in the Fc portion of an antibody
Pepsin
This protease cleaves antibodies multiple times below the disulfide bonds that connect the two heavy chains, resulting in one main fragment, the F(ab’)2 fragment, which contains who Fab fragments (and thus two antigen-binding sites) linked by disulfide bonds, and multiple fragments derived from the Fc portion of an antibody
Recombinant DNA technology and Antibody Structure
Permits one to modify the structure of an antibody molecule, for example to attach the constant region of a human Ig-gamma chain gene to the variable region of a murine Ig-gamma chain, in order to convey human effector functions to an antibody generated in mice against a human therapeutic antigen
Hinge Region of an Antibody and Flexibility
Hinge region linked the two Fab fragments and the Fc portion. Other portions of the antibody molecule, such as the region between the variable and constant domains are also flexible. Permits antibodies to interact with multiple identical antigens that are spaced at a variable distance on a surface
What Biochemical Structures Can Antibodies Interact With
Proteins, carbohydrates, nucleic acids, lipids, and small molecules
Antigens
Any substance that can be recognized by an antibody. Most but not all antigens can induce an antigen specific immune response when introduced into (by immunization or vaccination, typically in the context of an adjuvant that induces activation of the innate immune system; AlOH) animals or human subjects
Immunogens
Antigens that can induce an antigen-specific immune response when introduced (by immunization or vaccination, typically in the context of an adjuvant that induces activation of the innate immune system) into animals or human subjects
Haptens
Antigens such as small organic chemicals (e.g trinitrophenol) can be recognized by antibodies but cannot elicit an antibody response when injected by themselves. Can be converted to immunogens by conjugating them to a carrier proteins
Hypervariable Regions
With regard to immunoglobulin heavy and light chains and stretches of amino acids, where variability is concentrated: Three highly variable regions, which can be identified in the variable region of both the heavy and light chains, separated from less variable regions (framework regions). Clustered within three loops at the outer edge of the immunoglobulin domain, forming the antigen-binding site
Framework Regions
Less variable regions and separated from the hypervariable regions, of which there are four in both the heavy and light chains
Complementary Determining Regions (CDRs)
Refers to the six hypervariable regions, as they form a surface complementary to the antigen. The third complementarity determining regions (CDR3), which have the highest variability, are most critical for interaction with antigen
Epitope
The particular area recognized within the antigen by the antibody
Continuous/Linear vs. Discontinuous/Conformational Epitope
Antibodies can bind to antigens in their native or denatured form. Epitopes within a native protein can be contained either within the same stretch of amino acids (continuous or linear epitope) or more comonly within different parts of the polypeptide chain that are brought together in the folded protein (discontinuous or conformational epitope)
Forces That Bind Antibody/Antigen Interactions
Non-covalent forces: electrostatic, hydrogen bonding, Van der Waals interactions and hydrophobic interactions
Bruton’s Tyrosine Kinase & X-Linked Agammaglobulinemia (XLA)
Individuals with a genetic mutation in an X-linked kinase called Bruton’s tyrosine kinase (BTK), involved in B Cell signaling, develop X-linked agammaglobulinemia (XLA). Lack B-Cells and suffer from recurrent bacterial and viral infections. Antigen binds membrane bound Ig (cross-linking RTK). Noral Btk phosphorylates PLC-gamma which increases cystolic calcium levels which increases NFAT TF and DAG which activates PKC and then NF-kB
How Do Antibodies Enter Most Tissues
Antibodies enter most tissues via simple diffusion
How are IgA Antibodies Transported
Can be transported across epithelia for deivery to mucosal sites such as the lung and intestine
First Antibodies to be Generated
First antibodies to be generated are of the IgM class
Shape, Presentation, Function of IgM Antibodies
Form pentamers with a total of 10 antibody-binding sites, capable of binding with multivalent antigens in blood, at lower concentrations in lymph, and at very low levels in tissues. Particularly adept at activating the complement system
IgG Antibody
Activated during a second immune response, which can diffuse into tissues. Will often have undergone affinity maturation and will therefore have increased affinity for antigens. Most important antibody class in blood and tissues and confers immunity to neonates because it can cross the placenta (half-life is 2-3 weeks), so it provides protection in the neonate for up to 6 months. Also effective in activating complement and opsonizing pathogens for uptake via phagocytes
IgA Antibody
Activated during a second immune response, which can diffuse into tissues. Will often have undergone affinity maturation and will therefore have increased affinity for antigens. Dimeric form most common found in secretions, including mucosal secretions in the lungs, gut, saliva, and tear glands, and in breast milk
IgE Antibody
Acitvated during a second immune response, which can diffuse into tissues. Will often have undergone affinity maturation and will therefore have increased affinity for antigens. Plays a key role in allergic reactions and are present at very low levels in blood and tissues, but are typically bound with receptors on mast cells found beneath the skin and mucosal surfaces, and around blood vessels in connective tissue
Five Different Effector Functions Mediated by Antibodies
Neutralize pathogens and toxins
Activate complement
Opsonize pathogens
Promote antibody-dependent cell-mediated cytotoxicity (ADCC) in NK Cells
Activate Mast cells, basophils, and eosinophils
The latter three functions involve interactions of antibodies with Fc receptors expressed by distinct cell types
Neutralization of Pathogens and Toxins by Antibodies
Pathogens often bind with host cells via specific receptors (called adhesins for bacteria or attachment proteins for viruses) and toxins (derived from bacteria, insects, or snakes), similarly interact with specific host receptors. Can be interrupted with antibodies of the IgG or IgA classes, thus neutralizing the pathogen or toxin. Vaccines often designed to elicit neutralizing antibodies
Complement Activation by Antibodies
When bound with antigens on pathogen surfaces (IgM and IgG) antibodies undergo a conformational change in their Fc portion that permits binding of C1q of the classical complement pathway. Activation of complement in this manner can lead to activaiton of the MAC, induction of inflammation, opsonization of pathogens, and clearance of immune complexes
Opsonization By Antibodies
When bound with antigens on pathogen surfaces IgG antibodies can bind with Fc-gamma receptors on phagocytes. Engagement and cross-linking of multiple Fc-gamma receptors on phagocytes lead to the ingestion and destruction of pathogens
Induction of ADCC in NK Cells By Antibodies
Pathogen derived proteins can be expressed at the surface of infected cells and become targets for recognition by antibodies. Likewise, autoimmune responses often result in generation of antibodies directed against autologous surface antigens. Cells bound by IgG antibodies can be recognized by Fc-gamma receptors expressed by NK cells and trigger target cell destruction
Activation of Mast Cells, Basophils, and Eosinophils By Antibodies
Mast cells, basophils, and activated eosinophils express Fc-epsilon receptors that can interact with IgE antibodies. IgE antibodies can bind with these receptors even in the absence of antigen. Engagement of multivalent antigen with IgE on mast cells then leads to cross-linking of the Fc-epsilon receptors and rapid release of inflammatory mediators such as histamine. Typical antigens that trigger IgE responses include allergens and parasitic worms
How is the Variable Domain of an Immunoglobulin Heavy or Light Chain Encoded
Encoded by more than one gene segment
Encoding of Variable Domain of Light Chain
Variable domain is encoded by a variable or V gene segment and a shorter joining or J gene segment
Encoding of Variable Domain of Heavy Chain
Variable domain is composed of a V gene segment, a short diversity (D) gene segment and a J segment
Rearrangements To Produce Immunoglobulin Heavy and Light Chains
The rearrangements that produce immunoglobulin heavy and light chains involve random selection of individual V, D, and J gene segments
Assembly of Light Chain and Heavy Chain
Assembly of the light chain involves a single joining step between a V and J gene segment, whereas assembly of the heavy chain involves two joining steps, first D to J and then V to D-J
What Follows Gene Rearrangments of Heavy and Light Chains
Following gene rearrangement, genes are transcribed and the primary transcript is spliced to remove introns
CDR1, CDR2, and CDR3
The V region genes encode areas of the heavy and light chains that include the complementary determining regions 1 and 2 (CDR1 and CDR2), whereas the joints between the V, D, and J elements encompass CDR3
Why is the CDJ Recombination Process Highly Regulated
Highly regulated so that each B cell only expresses a single productively rearranged antibody receptor
Where Does Rearrangement Occur First and Second
Rearrangement of one allele at the heavy chain occurs first and if this is successful, rearrangement at the light locus is initiated
How is the Assembly of Gene Segments Guided
Guided by DNA sequences, called recombination signal sequences that flank the individual gene segments
What Does Each Recombination Signal Sequence Consist Of
Each recombination signal sequence consists of a conserved sequence of 7 nucleotides (a heptamer) and a conserved sequence of 9 nucleotides (a nonamer), separated from each other by a non-conserved spacer sequence of either 12 nucleotides (approximately one turn of a DNA helix) or 23 nucleotides (approximately two turns of a DNA helix)
12/23 Rule (Immunoglobulin Production)
Recognition sequences containing a 12-nucleotide spacer can only recombine with a recognition sequence containing a 23-nucleotide spacer. Avoids erroneous rearrangment and permits DNA fragments to be rearranged in a highly ordered manner
VDJ Recombinase
In recombination, VDJ recombinase binds with the recombination sequences and cleaves DNA
RAG-1 and RAG-2
Two lymphocyte-specific proteins, which are essential for the VDJ recombination process
Severe Combined Immune Deficiency (SCID)
When human subjects with a genetic disruption in either RAG-1 or RAG-2 genes are unable to undergo VDJ recombination and thus lack mature B and T cells, resulting in SCID
Omenn Syndrome
On other subject, RAG genes are only partially disrupted, leading to a leaky phenotype, involving the non-physiological expansion of small populations of T cells, leading to inflammatory reactions similar to those seen in graft-versus-host disease (a complication of bone marrow or stem cell transplantation)
Imprecision of Joining of Different Gene Segments in Immunoglobulin Production
A key process of VDJ recombination. Enzymes can either take away or randomly add nucleotides at the joints. The random addition of nucleotides, often called N-nucleotides, by the enzyme TdT plays a particularly important role. Dramatically increases antigen receptor diversity, but can often result in the generation of non-functional proteins
Enzyme Terminal Deoxynucleotidal Transferase (TdT)
Is responsible for increasing diversity by either taking away or randomly adding nucleotides at the joints of the heavy and light chains. Addition of N-nucleotides can dramatically increase antigen receptor diversity, but often results in the generation of a non-functional proteins
Erroneous Targeting of the VDJ Rearrangement Process
Can result in chromosomal translocations, which are present in a large number of B cell (and sometimes T cell) tumors
Burkitt Lymphoma
Involves a translocation of the immunoglobulin heavy or light chain promoter/enhancer to the myc oncogene, resulting in uncontrolled myc expression. Also involves Epstein-Barr virus infection of B cells, as well as immune suppression, commonly associated with malaria
Two Principle Mechanisms That Generate Diversity in Antibody Receptors Prior to Antigen Exposure to B Cells
Combinatorial diversity and junctional diversity
Combinatorial Diversity
There are multiple different copies of distinct gene segments (V, D, and J segements) that can be combined in a random manner. In addition, heavy and light chains can pair in many different combinations
Junctional Diversity
This is introduced at the joints between the gene segments as a result of removal and addition of nucleotides during the recombination process
Regulation of VDJ Recombination and Allelic Exclusion
Receptor gene assembly is initiated on only one allele of the heavy chain locus. If this leads to a successful rearrangement, rearrangement of the other heavy chain allele is prevented in a process called allelic exclusion, and rearrangement is initiated at one allele of the k light chain locus. Should rearrangement at the heavy chain locus fail, rearrangement at the other allele will be initiated. If rearrangement at the second heavy chain is also non-successful, further rearrangement is halted and the immature B cell will be targeted for death by apoptosis. Same thing happens with light chains at kappa first and then lambda. Processes are in place in the bone marrow to week out many self-reactive B cells. Additional mechanisms are in place in the periphery to prevent the activation of autoreactive B cells that escaped the weeding out process in the bone marrow
High-Avidity Interactions
Often occurs with surface receptors, antigens with repeated structures, or soluble antigens expressed at high levels. Such strong interactions lead to apoptosis (clinal deletion) of the autoreactive B Cell. Sometimes, such autoreactive B Cells obtain a second change and re-express the RAG genes to undergo secondary VDJ rearrangements (with deletion of the autoreactive receptor) in the hope of generating a non-autoreactive receptor, in a process called receptor editing. If the new receptor is autoreactive as well, the B Cell will be deleted
Intermediate-Avidity Interactions
This may occur against most soluble self-proteins. Such B Cells are functionally inactivated or anergized. Such anergic B Cells may leave the bone marrow but do not react against antigens and may eventually die
Low-Avidity Interactions
If receptors recognize self-antigens present in bone marrow at very low levels, the B cells may survive and be exported to the periphery. Such B Cells are unaware or ignorant of the self-antigen they recognize
No Self-Reactivity
Such B Cells are exported to the periphery and will differentiate further to full maturity
How are B Cells Activated to Secrete Antibodies
Some activated B cells will differentiate into plasma cells that secrete large amounts of antibodies. Plasma cells typically migrate to bone marrow or the mucosal immune system, where they might produce antibodies for several weeks. Following infection or vaccination, small numbers of antigen-specific B cells will continuously differentiate into plasma cells even after the pathogen or immunizing antigen has been long cleared. This process is critical for the generation of neutralizing antibodies against many pathogens and the effectiveness of most vaccines
How are immunoglobulins switched from the membrane to the secreted form
Switching of the immunoglobulins from the membrane to the secreted form is accomplished by differntial RNA processing
Somatic Hypermutation
Following activation in the presence of T cell help, B cells within germinal centers of peripheral lymphoid organs can undergo point mutations within the variable region gene segments, this is called “somatic hypermutation”
Activation-Induced Deaminase (AID)
Enzyme responsible for somatic hypermutation. Mutations might result in decreased, similar, or increased affinity of the antibody with its cognate antigen
Where do B Cells Expressing Surface Immunoglobulin With Increased Affinity for Antigen Bind
B Cells expressing surface immunoglobulin with increased affinity for antigen will bind more avidly with antigen displayed on the surface of follicular dendritic cells in germinal centers and will show a proliferative advantage
Affinity Maturation of the Antibody Response
Greater avidity of B cells will result in the selective survival of B cells expressing antigen receptors with the highest affinity for antigen (evolution on a microscale), this is known as affinity maturation of the antibody response
Repeated Immunizations
Because the antigen-binding site of an antibody is formed by CDR1, CDR2, and CDR3 regions within heavy and light chains, repeated immunizations result in enrichment of mutations within the CDRs, germinal center reaction causes antibody resopnses to improve over time
First Antigen Receptors Expressed By B Cells
IgM and IgD varieties
First Antibody Secreted During an Immune Response
IgM
Class/Isotype Switching
Later in the immune response, antibodies with the identical antigen-specificity (i.e the same heavy and light chain variable domains) may be of the IgG, IgA, or IgE variety, known as class or isotype switching
Requirements for Class/Isotype Switching
Requires prior B cell activation and T cell help
Switch Region of DNA/Class Switch Recombination/Selection of the Switch Region
At the molecular level, each immunoglobulin heavy chain constant region gene fragment is preceded by a stretch of repetitive DNA, called a switch region, that guides a recombination process, called a class switch recombination. When a B cell switches from the co-expression of IgM and IgD to the expression of another isotype, DNA recombination occurs between the switch region upstream of Ig-mu to another Ig gene. AID, involved in somatic hypermutation, also plays a critical role in class switch recombination. Selection of the switch region is guided by cytokines produced by other immune cells, in particular antigen-experienced, CD4-expressing T lymphocytes
Number of Rounds of Class Switching Recombination B-Cells Might Undergo
Individual B Cells might undergo more than one round of class switch recombination. T cells often produce a mixture of cytokines, resulting in divergent class switching in individual B Cells with the same antigen specificity
